The common bean (Phaseolus vulgaris L.), also known as the string bean, field bean, flageolet bean, French bean, garden bean, green bean, haricot bean, pop bean, snap bean, or snap, is a herbaceous annual plant grown worldwide for its edible dry seed (known as just “beans”) or unripe fruit (“green beans”). Its botanical classification, along with other Phaseolus species, is as a member of the legume family Fabaceae. Wild P. vulgaris is native to the Americas and was domesticated separately in Mesoamerica and in the southern Andes region. This provides the basis for the domesticated common bean having two gene pools.
The main categories of common beans, as characterized by their use, are dry beans, which are seeds harvested at complete maturity, snap beans, which are tender pods with reduced fiber harvested before the seed development phase, and shell beans, which are seeds harvested at physiological maturity.
The common bean is a highly variable species with a long history of cultivation. Over 130 varieties of common beans are known. All wild members of the species have a climbing habit. Most cultivars are classified as “pole beans” or “bush beans” depending on their growth habits. Pole beans have a climbing habit and produce a twisting vine, which must be supported by poles, trellises, or other means. Bush beans are short plants that grow to not more than 2 feet (61 cm) in height, often without needing support to grow. Bush beans generally reach maturity and produce all of their fruit in a relatively short period of time, then cease to produce.
There are many varieties specialized for use as green beans due to the succulence and flavor of their pods. These varieties are usually grown in home vegetable gardens. Pod color can be green, yellow, purple, red, or streaked. Shapes range from thin “fillet” types to wide “romano” types and more common types in between. Examples of bush (dwarf) types include, but are not limited to, ‘Blue Lake 274’, ‘Bush Kentucky Wonder’, ‘Derby’, ‘Dwarf French Bean Seeds—Safari (Kenyan Bean)’, and ‘Purple Teepee’. Examples of pole type green beans include, but are not limited to, ‘Algarve French Climbing Bean’, ‘Blue Lake FM-1 Pole Bean’, ‘Golden Gate Pole Bean’, ‘Kentucky Blue Pole Bean’, and ‘Kentucky Wonder’.
Volatile compounds provide the primary source of flavor in common beans. Common beans are known to produce at least a hundred volatile compounds in their pods (Barra et al., 2007). Flavor volatiles are derived primarily from three biosynthetic pathways in plants (Lewinsohn et al., 2001). The three pathways are those for fatty acids, carotenoids/terpenoids, and the phenylpropanoid/shikimic acid. The fatty acid pathway begins with acetyl CoA and proceeds through palmitic acid, stearic acid, and oleic acid. Oleic acid is converted in the plastids to linoleic acid and linolenic acid through the action of desaturases. Linoleic and linolenic acids are, in turn, converted to volatile compounds important to flavor through the action of a lipoxygenase followed by a hydroperoxide lyase (Noordermeer et al., 2001). This pathway leads to the majority of flavor volatiles in common beans, such as 1-octen-3-ol, 1-penton-3-one, 1-penten-3-ol, hexanal, 1-hexanol, 2-hexenal, and 3-hexen-1-ol (De Lumen et al., 1978). Alternatively, acetyl CoA can be used in either the melavolate or non-melavolate pathway for terpenoid synthesis (Dubey et al. 2003). The melavolate pathway and non-melavolate pathway result in isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP and DMAPP are believed to be interchangeable through an isomerase and are the substrates for geranyl diphosphate synthase to produce geranyl diphosphate (GPP). GPP can either be used to produce monoterpenes, such as linalool, or undergo additional enzymatic changes to produce sesquiterpenes, carotenoids, or polyterpenes. The breakdown of carotenoids by the carotenoid cleavage dioxygenase I (CCD1) enzyme results in β-ionone (Wei et al., 2011). Both linalool and β-ionone are known to be present in common bean pods. Finally, the shikimic pathway followed by the phenylpropanoid pathway generates numerous volatile compounds in addition to an array of other compounds, such as flavonoids, lignans, esters, coumarins, and stilbenes (Vogt, 2010).
Early research on the genetics of flavor in snap beans was focused on linalool and 1-octen-3-ol because these compounds were present in variable amounts depending on the bean cultivar, and because these compounds appeared to be important to the characteristic flavor of snap beans (Stevens et al., 1967a; Toya et al., 1976). The results of crosses of beans expressing linalool and 1-octen-3-ol suggested that the amount of these two compounds in a bean were controlled by a small number of loci. This early genetic research was particularly focused on several Blue Lake commercial lines, which share a common ancestry with significant inheritance from the :Mesoamerican center of domestication.
There is little known about the inheritance of flavor traits in common beans other than two early studies by Stevens et al. (1967a) and Toya et al. (1976). These studies predate the advent of molecular markers in plant breeding and did not identify quantitative trait loci (QTL), SNPs, or even chromosomes related to the inheritance of flavor traits in common beans. Moreover, Stevens and Toyo disagreed on the number of loci present, but did show that linalool and 1-octen-3-ol levels are heritable traits.
The common bean is a diploid species with 22 chromosomes (Sarbhoy 1978; Maréchal et al. 1978). The chromosomes are small in size and similar in morphology. The genome size of P. vulgaris is about a 580 Mbp/haploid genome (Bennett and Leitch 2005). The genome relates to two distinct evolutionary lineages, i.e., Andean and Mesoamerican, that predate domestication (Debouck et al. 1993; Kami et al. 1995). The genome sequence of common bean (P. vulgaris L.) was published in 2014 by Schmutz et al. It is also published by Phytozyme, which is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. The Phytozyme genome for the common bean is published as Phaseolus vulgaris, v2.1 (Common bean), see, Phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris, and is incorporated herein by reference. This published genome includes about 27,433 total loci containing 36,995 protein-coding transcripts. See, Phytozyme: Phaseolus vulgaris, v2.1. In the common bean, the levels of duplication and the amount of highly repeated sequences are generally low. Early mapping experiments demonstrated that most loci are single copy (Vallejos et al. 1992; Freyre et al. 1998; McClean et al. 2002).
With the emergence of the genomic era in the field of common beans, it became possible to conduct genome wide association study (GWAS) mapping of this important crop. Due to the amount of recombination events over time in a natural population in comparison to the limited number of recombination events in a biparental cross, GWAS tends to give higher genomic resolution in comparison to linkage mapping studies. GWAS mapping is also faster because a study can be completed in a single season on an established population of beans, in comparison to the need to grow multiple generations to perform biparental linkage studies.
The flavor of green beans involves complicated interactions between different volatiles. This makes the task of breeding flavor qualities associated with volatiles into later generations challenging. In this regard, the goal of developing new common bean cultivars requires evaluation of parents and the progeny of crosses in the F1, F2, or later generations. To reach this goal, a breeder must carefully select and develop plants that have desired flavor traits in cultivars. The absence of predictable success of any given cross requires that a breeder make several crosses with different breeding objectives, all of which is time consuming, costly, and requires growth time and space, pedigree selection, and numerous crossing and backcrossing steps. To date, bean breeders have typically focused on traits with simpler genetics as compared to flavor traits, and a more immediate impact on the bottom line, such as high yield.
Thus, there is an ongoing need for the development of stable, high yield cultivars of common beans that express superior flavor quality traits, as well as the identification and development of molecular markers for genes relevant to flavor traits, and methods of using flavor-specific molecular markers for refining bean breeding schemes to develop superior cultivars having high quality taste. For example, it would be extremely helpful if bean breeders could use molecular markers to determine whether genes relating to specific flavor traits are present in any given common bean population, then use the presence or absence of certain genes in a common bean population to develop efficient breeding designs. Molecular markers for flavor volatiles would allow selection of superior lines in early generations, without wasting time or space on poor selections. It would provide an objective measure to identify the selections because the ability of a plant breeder to actually taste hundreds or thousands of potential selections in the field is highly limited and impractical. Indeed, molecular markers, e.g., a SNP, a SNP flanking sequence, a PCR primer(s) for a SNP, could be beneficial for use in marker assisted identification of candidate bean populations and marker assisted selection for efficient breeding. SNP markers are direct marker systems for tagging genes and could be used to rapidly identify genes in plants that express desired flavor traits.